Commit c1ff1988 by Jean-Yves TINEVEZ

### Update user doc after plotting functions renaming.

parent 3a6f69f5
 ... @@ -10,6 +10,7 @@ We give here the list of properties stored in the DeProj classes and their defin ... @@ -10,6 +10,7 @@ We give here the list of properties stored in the DeProj classes and their defin * [boundary](#boundary) * [boundary](#boundary) * [center](#center) * [center](#center) * [junction_ids](#junction_ids) * [junction_ids](#junction_ids) * [n_neighbors](#n_neighbors) * [area](#area) * [area](#area) * [perimeter](#perimeter) * [perimeter](#perimeter) * [euler_angles](#euler_angles) * [euler_angles](#euler_angles) ... @@ -132,6 +133,10 @@ j = ... @@ -132,6 +133,10 @@ j = ### `n_neighbors` How many neighbours have a cell. Note that for cells on the border of the tissue, we try to deal with border effects. For a cell at the border, we count the number of neighbours including all cells, even the ones not drawn because they are cropped by the image borders. ### `area` ### `area` The area of the apical surface of the cell, delimeted by its boundary. This value reports the 3D area, of the de-projected cell on the tissue surface. Units are physical units; if you used a pixel size in µm, the area will be in µm². The area of the apical surface of the cell, delimeted by its boundary. This value reports the 3D area, of the de-projected cell on the tissue surface. Units are physical units; if you used a pixel size in µm, the area will be in µm². ... @@ -298,7 +303,7 @@ We can use this junction graph to plot a topological representation of the segme ... @@ -298,7 +303,7 @@ We can use this junction graph to plot a topological representation of the segme % Get the junction graph (run the RunExample.m file first) % Get the junction graph (run the RunExample.m file first) g = dpr.junction_graph; g = dpr.junction_graph; % Display the junction graph. We use the graph builtin plot method. % Display the junction graph. We use the graph builtin plot method. We just use a 2D plot. >> plot( g, ... >> plot( g, ... 'XData', g.Nodes.Centroid(:,1), ... 'XData', g.Nodes.Centroid(:,1), ... 'YData', g.Nodes.Centroid(:,2), ... 'YData', g.Nodes.Centroid(:,2), ... ... @@ -308,6 +313,10 @@ g = dpr.junction_graph; ... @@ -308,6 +313,10 @@ g = dpr.junction_graph; 'Marker', 'o', ... 'Marker', 'o', ... 'MarkerSize', 4, ... 'MarkerSize', 4, ... 'NodeColor', 'r' ) 'NodeColor', 'r' ) % Another simpler solution is to directly use a special deproj plotting method. % This one plots the junction graph in 3D, with white edges. Uncomment it to try. % dpr.plot_values_junction( 'w', gca ) ``` ``` ![PlotJunctionGraph_1](static/PlotJunctionGraph_1.png) ![PlotJunctionGraph_1](static/PlotJunctionGraph_1.png) ... ...

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